[R-sig-eco] marginal vs sequential results of lme

[Ben Bolker]

On 11-01-20 12:24 PM, Iannone, Basil wrote:
> Dear R users,
> 
> I am having a problem with interpreting "anova" results of a linear mixed
> effects model.
> 
> The data I am analyzing is from study that was set up as a randomized
> block design with two factors at two levels. The model is:
> 
>        m1 <- lme(Y~A*B, random = ~1|Block)
> 
> The design is completely balanced and no data are missing. When I run a
> sequential anova I get a p-value = 0.02 for factor B. When I run a
> marginal anova (specified by "type = "marginal""), I get a p-value = 0.29
> for factor B. The model summary ("summary (m1)" ) agrees with the marginal
> test and shows a p-value = 0.29 for factor B. Further when I graph values
> of Y against levels of B, I see no difference.
> 
> I thought that sequential and marginal anovas should produce the same
> results when the design is balanced. Can someone please explain to me why
> the results of the "anova(m1)" differ from the results of "anova(m1, type
> = "marginal")" and "summary(m1)."
> 
> Thanks for your help,

   Haven't spent a lot of time thinking this through, but I'm guessing
that the problem is with the interaction term.
   Can you give a reproducible example (to save me the trouble of making
one up)?